South Africa hit back on Wednesday against charges of xenophobia after protests against undocumented migrants and said African nations should address issues like instability causing their people to leave.

A series of anti-migrant protests in recent weeks across Africa's most industrialised country, along with claims of attacks against foreigners, have prompted Nigeria and Ghana to voice concern.

"South Africans are not xenophobic," presidential spokesperson Vincent Magwenya told reporters. "What you have is pockets of protest, which is permissible within our constitutional framework."

In fresh demonstrations on Wednesday, hundreds of people marched in the eastern city of Durban and other centres to demand that the government take action against undocumented migrants operating businesses such as small shops.

'Continent needs to work together': Presidents Ramaphosa, Chapo

Demonstrations in previous months have also sought to deny undocumented foreigners access to South African clinics and hospitals.

In talks on Tuesday, Mozambique's President Daniel Chapo and South Africa's President Cyril Ramaphosa had agreed "the continent needs to work together to address the issues that are behind these levels of migration", the spokesperson said.

These included "conflicts, issues of instability, and in some areas... the misgovernment that causes people to migrate in large numbers and seek refuge in different parts of the continent, including South Africa."

There should "be willingness to constructively engage on what are these issues and factors behind peoples seeking to leave their countries of birth and seeking refuge elsewhere", Magwenya said.

Emergency repatriation for Nigerians

Nigeria has announced emergency repatriation flights for its citizens living in South Africa and warned Pretoria on Monday that it was not doing enough to address anti-immigrant threats and harassment.

Ghana summoned South Africa's envoy in late April over several "xenophobic incidents."

Magwenya said the label of xenophobia was a "lazy" analysis that risked "unfairly maligning" South Africa in the same way as false US claims of a "genocide" against its white minority.